Finding that PDF

Unfortunately, not everyone has access to a massive research library (or in some cases, any research library at all). Yet, the literature is an essential part of any paleontologist's repertoire. In this post, I'll briefly review some options out there for locating free or low-cost scientific publications on the web.

• Google Search: Sometimes, all it takes is a quick Google search to find a paper. For instance, say I'm looking for Marsh's old paper on characters of Odontornithes. I type "Characters of the Odontornithes, with notice of a new allied genus" into the old Google search box, and what do you know? It gives me a link to Matt Wedel's archive of O.C. Marsh papers! Sometimes, of course, you might have to try a few variants on a search before you hit on the right PDF. Often, when I'm doing initial research on a topic, I'll type in "[taxon or topic name here] pdf". You never know what you might find! For instance, typing "Triceratops PDF" gave me a link to several very relevant papers. Google Scholar also works pretty well in this regard (and will often filter out most of the non-scholarly stuff).
• Google Books: I have had some real success, particularly with older works, on this search engine. I strongly recommend setting the search settings to only find books with "full view," if you're not interested in just snippets of text. Once the recent settlement with publishers gets worked out, I think we can expect some really good things in terms of low-cost access to out-of-print but in-copyright publications.
  
• Scribd: This website offers browsable documents for a surprising number of paleontological papers, although you must be a registered user (free) to download PDFs.
• Journal Archives: Many museum publications, such as Fieldiana and all of the AMNH publications, are available online. It's always worth checking out museum web pages to see if their old publications are out there. A number of journals also have freely available archives. 'Nuff said.
  
• Author's Web Page: More and more scientists have PDFs of their papers on their web page - so, it's always worth a quick search to see what's available.
  
• Writing the Author: If you can't find the PDF for a recently published article through other means, send an email to the author. As I mentioned in a previous post, it's a great ego boost for those of us who write scientific papers!

Of course, these suggestions probably aren't news to some of the more experienced paleontologists out there - but I do hope this is useful for those just beginning in the field. What other sites do you find particularly useful for this sort of background research?

Disclaimer: It is entirely up to the user to be aware of any copyright restrictions that may apply to the download or use of any of the resources addressed here.

Update: Dave Hone has posted a really nice continuation of this theme over at his blog.

Bone-ing Up on Allometry

Allometric scaling - roughly defined, when different parts of an organism grow at different rates - is an important factor in biology. In part, allometry describes how babies have relatively larger heads than adults (we exhibit negative allometry in this trait, because our skulls don't grow as quickly as the rest of the body) or how some crabs have gigantic claws (an example of positive allometry, in which the claw grows much faster than the rest of the body). Allometry (and its counterpart isometry, in which proportions don't change at all) can be examined on an intraspecific level, such as the example in humans, or on an interspecific level.

It's not cute - it's allometric!
Toronja Azul, Chihuahua Puppy, 5 August 2007 via Wikimedia Commons, Creative Commons Attribution 2.0

For paleontologists and biologists, allometry and isometry are particularly interesting when it comes to understanding groups with large ranges in body size. When you grow a Tyrannosaurus from an Eoraptor-like ancestor, what has to change in order to support the body mass? Sometimes it's postural - big animals tend to have more "columnar" posture (with the supporting legs straight beneath the body) and small animals tend to have more "flexed" posture. In other cases, it's allometric - big animals might tend to have relatively thicker bones than small animals. Sometimes, it might even be both. And sometimes, none of these comfortable patterns seem to fit perfectly.

Looking at Cats
Regardless of the patterns (and often because of them), scaling studies of limb bones have attracted a lot of ink over the years. A recent contribution, authored by Michael Doube and colleagues, appeared the other week in the open access journal PLoS ONE. Their paper, entitled "Three-dimensional geometric analysis of felid limb bone allometry," takes a novel peek at how different limb bones scale within cats. Cats are a particularly interesting study subject, because they span a range of adult body masses - from as little as 3 kg in the domesticated cat to 306 kg in the largest tiger.

Domesticated cat (left) and lion skeletons, scaled to roughly the same height at the shoulders.

Limb bone allometry in its own right is an interesting, but rather conventional, topic. Most studies are content to take some linear measurements, or perhaps a cross-section or two, for a range of species. Doube and colleagues did something unique - they examined the three-dimensional properties of entire limb bones, as well as two-dimensional properties in series along the entire bone, using CT scans coupled with custom-written software macros.

The macros (which are one of the really cool things about this paper, and a big reason for why I'm highlighting it here) calculate a variety of cross-sectional properties automatically from CT scan data. Previous macros (such as the very useful MomentMacroJ) required a human operator to do things one slice at a time. Believe me, this can take forever for a limb bone data set of 200 CT slices. The authors of the paper in question were able to quickly and efficiently assemble data sets for a variety of measurements from a variety of limb bones for a variety of felid species - over 16,000 CT slices in total! So, this allowed compilation of a database for measurements throughout the bone - not just at the boring old mid-shaft. Furthermore, they calculated joint geometries (through a sphere-fitting routine, to approximate surface area of certain joints) as well as moments of inertia for entire bones.

This data set allowed the authors to get one of the the most complete pictures of limb bone properties ever assembled. In general, cross-sectional properties at mid-shaft (a standard location for measurement) did not differ significantly from isometry (i.e., big cat bones look the same as little cat bones). Of course, a larger sample might achieve statistical significance at P less than 0.05 (results are suggestive, but don't differ significantly from isometry). Interestingly, joint surfaces and moments of inertia tend to scale with positive allometry. In other words, big cats have relatively bigger joints and beefier bones (a more thorough and accurate explanation of moments of inertia is beyond the scope of this post) than do small cats.

So why are these results interesting? Well, it appears that cats "get big" differently from other animals. Whereas comparably sized mammals tend to change from flexed limb postures to more columnar limb postures as body size increases, cats apparently maintain a relatively flexed posture across their size range. Instead, cats compensate for the change in body mass by beefing up their bones. Skeletal and postural responses to increased body size are pretty darned diverse, and there is no "one size-fits-all" solution. It will be very interesting to see broader applications of this methodology.

Open Source Solutions
The authors used ImageJ, an open source image processing system (detailed in a previous post here) for much of their data collection. The macro they wrote and used is also freely available with their paper--so feel free to try it out with your own data. Their massive datafiles were collated with MySQL, and the statistical analysis was conducted within R, using the SMATR package for regression analysis. So, it was an open source project from start to finish! As the cherry on top of the cake, publication in PLoS ONE means that the paper is easily and freely accessible to all. I've already made a few notes on the paper, with quick and gracious responses from one of the authors. If you have anything to add to the discussion, don't be shy!

Further Reading
If you're interested in more open source solutions to these sorts of problems, check out lead author Michael Doube's web page. He's got lots of macros, pretty pictures, and other goodies for enjoyment and download.

The Citation
Doube, M., Wiktorowicz-Conroy, A., Christiansen, P., Hutchinson, J., & Shefelbine, S. (2009). Three-dimensional geometric analysis of felid limb bone allometry. PLoS ONE, 4 (3) DOI: 10.1371/journal.pone.0004742

Lizard Skulls! (the update)

In a previous post, I noted a really nifty collection of digital lizard skulls available thanks to the efforts of Nick Gardner, writer of "why I hate theropods" and a student in the Casey Holliday lab. Well, it turns out that I jumped the gun just a little bit (thanks for nothing, Facebook!). . .the complete director's cut of the page is now available, and is highlighted in a posting here. Congratulations on a really great resource!

Two Items

First, congratulations to Dr. Mark Loewen, who successfully completed his dissertation defense on Tuesday afternoon. His dissertation focused on variation in Allosaurus, and was truly an epic piece of work.

Second, check out this paper that just came out in PLoS ONE. The paper covers some interesting aspects of limb bone allometry (shape changes with size), and provides open source macros for ImageJ, so you could do similar analyses on your own dataset. In the next day or two, I should have more to say, but for the time being check out the link. . .as always, the papers are free to download, and please take advantage of the commenting/note-making/rating features on the PLoS website.

Doube M, Conroy AW, Christiansen P, Hutchinson JR, Shefelbine S (2009) Three-Dimensional Geometric Analysis of Felid Limb Bone Allometry. PLoS ONE 4(3): e4742. doi:10.1371/journal.pone.0004742

3D Slicer: The Tutorial Part VI

Nick (of why I hate theropods) posted a question today on this blog, asking if there was a way to save models from Slicer as STL files. So, here's a quick post explaining how to do just this.

Why would you want to do this, if there's a perfectly good VTK-format model exported by Slicer already? Well, VTK is an industry standard that is good for many open source software packages, but most commercial packages don't deal well with the format. So, STL ("stereolithography") files are a happy medium. STL format has its own issues, but is nearly universally read by computer modeling programs.

In order to get a start on exporting STL's from Slicer, let's return to where we picked up from the last tutorial. Load all of your files (you saved the model and label map after the last tutorial, right?). This should give you the brain in the middle of the 3D viewer. For some unknown reason, say you want to export this brain as an STL for post-processing in another program. Luckily, it's a relatively easy thing to do!

First, switch to the "Models" module, by selecting under the "Modules" drop-down menu.
Then, click on the "Save" tab, to expand this option. Hit the "Save Model" button.

A dialog box comes up, and you can choose an alternative from the default (VTK) under the "Files of Type" option. In this case, select "STL."
Choose the name and location for your file, hit save, and you're done!

PLoS ONE's newest editor

It's official. . .I have just accepted an invitation to join the editorial board for the on-line, open access journal PLoS ONE. With its recent burst of vertebrate paleontology articles (featured prominently in their Paleontology Collection), the future is looking quite bright. I am very eager to assist the open access movement in a more concrete way, for a journal that is making many positive changes to the way research is communicated. Other vertebrate paleontologists on the editorial board include Tom Kemp, Paul Sereno, and David Unwin (and my apologies to anyone else I neglected to mention).

So. . .bring on the manuscripts!

Crouching Theropod, Hidden Dragon

Fossil footprints (falling in the general category of "ichnofossils") reveal a wealth of information about dinosaur biology, such as speed, posture, and behavior. These traces are particularly useful when offering information independent from, but consistent with, hypotheses derived from purely anatomical studies.

Today, a new paper in the open access journal PLoS ONE presents an unusual set of theropod (meat-eating dinosaur) ichnofossils from the Early Jurassic-aged Moenave Formation of southwestern Utah. The tracks are preserved within the St. George Dinosaur Discovery Site at Johnson Farm, a massive facility housing thousands of footprints (for additional scientific publications and background on the site, refer to this page). But, if there are thousands of footprints known at the site (in addition to the thousands known from other sites throughout the world), what makes the fossils featured in the paper so special?

Theropods were bipedal animals, and known ichnofossils typically only preserve evidence of the hindlimb. But, one specimen in particular at the St. George locality preserves impressions of the hind feet, forefeet, and the rear end of a lazy carnivore. A resting trace!

Artist's conception of the St. George trackmaker at rest. Note in particular the resting posture and the orientation of the hands. From Milner et al. 2009; painting by Heather Kyoht Luterman.

Yet, even resting traces aren't completely unheard of for theropod dinosaurs. The really interesting thing here is that the specimen preserves relatively unambiguous impressions of the hand posture. The animal was resting with its hands turned inward, and the outer surfaces of the fingers and wrist (rather than the palms) touching the substrate.

Why does this matter? Well, it all has to do with reconstructions of forelimb mobility and posture. Old reconstructions of theropod dinosaurs showed them walking around with palms down (think of an alligator dragged upright); later work has strongly suggested that the palms faced inward, more like birds.

Traditional restoration of two theropods, by Charles R. Knight. Note the palm-down, rather than palm-in, posture of the hands.

So, the new St. George tracks are the first good ichno-evidence of forelimb posture in theropod dinosaurs. Furthermore, and perhaps most importantly, it suggests that this posture evolved pretty early on, in some of the first theropod dinosaurs.

As the authors note, anatomical reconstructions of forearm movement have primarily focused on more "derived" theropods (animals from the Late Jurassic and beyond). It would be really, really nice to get additional studies on the anatomical structures of the forelimb in animals like Dilophosaurus and Coelophysis (Ken Carpenter did get a good start on this a few years back; see his 2002 paper, "Forelimb biomechanics of nonavian theropod dinosaurs in predation." Senckenbergiana Lethaea 82: 59-76). Also, paleontologists will want to be on the lookout for similar traces. Is the specimen described here typical, or an individual anomaly? The authors reviewed other alleged resting traces from theropods, but considered that most of them were either misidentified or too poorly preserved to offer usable information. Finally, does resting posture of the forelimbs necessarily reflect what the animals were doing the other 99 percent of the time?

Congratulations to the authors on a stimulating paper. If you have an opinion on this research, don't just post it in the blog's comment section (although please do that, too). Head over the the PLoS ONE website, and register your own comments, notes, and ratings on the article!

The Reference
Andrew R. C. Milner, Jerald D. Harris, Martin G. Lockley, James I. Kirkland, Neffra A. Matthews (2009). Bird-Like Anatomy, Posture, and Behavior Revealed by an Early Jurassic Theropod Dinosaur Resting Trace. PLoS ONE, 4 (3) DOI: 10.1371/journal.pone.0004591